# Bio.ExPASy.Prosite module

Parser for the prosite dat file from Prosite at ExPASy.

See https://www.expasy.org/prosite/

Tested with:

  - Release 20.43, 10-Feb-2009

  - Release 2017_03 of 15-Mar-2017.

Functions:

  - read Reads a Prosite file containing one Prosite record

  - parse Iterates over records in a Prosite file.

Classes:

  - Record Holds Prosite data.

Bio.ExPASy.Prosite.parse(handle)

  Parse Prosite records.

  This function is for parsing Prosite files containing multiple records.

  Arguments:

    - handle - handle to the file.

Bio.ExPASy.Prosite.read(handle)

  Read one Prosite record.

  This function is for parsing Prosite files containing exactly one record.

  Arguments:

    - handle - handle to the file.

class Bio.ExPASy.Prosite.Record

  Bases: `object`

  Holds information from a Prosite record.

  Main attributes:

    - name ID of the record. e.g. ADH_ZINC

    - type Type of entry. e.g. PATTERN, MATRIX, or RULE

    - accession e.g. PS00387

    - created Date the entry was created. (MMM-YYYY for releases before January 2017, DD-MMM-YYYY since January 2017)

    - data_update Date the ‘primary’ data was last updated.

    - info_update Date data other than ‘primary’ data was last updated.

    - pdoc ID of the PROSITE DOCumentation.

    - description Free-format description.

    - pattern The PROSITE pattern. See docs.

    - matrix List of strings that describes a matrix entry.

    - rules List of rule definitions (from RU lines). (strings)

    - prorules List of prorules (from PR lines). (strings)

  NUMERICAL RESULTS:

    - nr_sp_release SwissProt release.

    - nr_sp_seqs Number of seqs in that release of Swiss-Prot. (int)

    - nr_total Number of hits in Swiss-Prot. tuple of (hits, seqs)

    - nr_positive True positives. tuple of (hits, seqs)

    - nr_unknown Could be positives. tuple of (hits, seqs)

    - nr_false_pos False positives. tuple of (hits, seqs)

    - nr_false_neg False negatives. (int)

    - nr_partial False negatives, because they are fragments. (int)

  COMMENTS:

    - cc_taxo_range Taxonomic range. See docs for format

    - cc_max_repeat Maximum number of repetitions in a protein

    - cc_site Interesting site. list of tuples (pattern pos, desc.)

    - cc_skip_flag Can this entry be ignored?

    - cc_matrix_type

    - cc_scaling_db

    - cc_author

    - cc_ft_key

    - cc_ft_desc

    - cc_version version number (introduced in release 19.0)

  The following are all lists if tuples (swiss-prot accession, swiss-prot name).

  DATA BANK REFERENCES:

    - dr_positive

    - dr_false_neg

    - dr_false_pos

    - dr_potential Potential hits, but fingerprint region not yet available.

    - dr_unknown Could possibly belong

    - pdb_structs List of PDB entries.

  __init__()

    Initialize the class.

  __firstlineno__ = 61
  __static_attributes__ = ('accession', 'cc_max_repeat', 'cc_site', 'cc_skip_flag', 'cc_taxo_range', 'created', 'data_update', 'description', 'dr_false_neg', 'dr_false_pos', 'dr_positive', 'dr_potential', 'dr_unknown', 'info_update', 'matrix', 'name', 'nr_false_neg', 'nr_false_pos', 'nr_partial', 'nr_positive', 'nr_sp_release', 'nr_sp_seqs', 'nr_total', 'nr_unknown', 'pattern', 'pdb_structs', 'pdoc', 'postprocessing', 'prorules', 'rules', 'type')

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